nf-core/panoramaseq
a pipeline to process sequencing based spatial transccriptomics data from in-situ arrays
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to additional FASTA file to concatenate with main genome (optional).
string^\S+\.fn?a(sta)?(\.gz)?$Do not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringMerge all count TSV files into a single H5AD file with spatial coordinates.
booleanCSV file with spatial coordinates (cell, x, y) for merging count data.
stringValidate the structure of the merged H5AD file.
booleanSkip MultiQC report generation.
booleanBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Base URL or local path to location of modules test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringPipeline-specific parameters for STAR, UMI-tools, and GPU settings.
Path to the STAR genome index directory.
stringPath to the GTF annotation file for STAR.
stringNumber of reads to subsample with seqtk. If not set (null), no subsampling is performed.
integer,nullUMI-tools extract method (e.g. ‘regex’, ‘tagged’, ‘string’).
stringBarcode pattern for UMI-tools.
stringWhether to extract UMI (true/false).
booleanSecond barcode pattern for UMI-tools (optional).
string,nullUMI separator for UMI-tools (optional).
string,nullStart position of the barcode in the read (zero-based).
integer9QUIK barcode calling strategy (e.g., ‘4_7_mer_gpu_v1’, ‘accurate’).
string4_7_mer_gpu_v1Distance measure for barcode matching.
stringNumber of GPUs to use.
integer